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| Status |
Public on Jul 01, 2013 |
| Title |
macrophages double-KOs #4 |
| Sample type |
SRA |
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| Source name |
mouse peritoneal macrophages
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 17 weeks
gender: female
cell type: peritoneal macrophage
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed immediately in µMACS™ mRNA Isolation Kit lysis buffer and cleaned with with LysateClear Columns (Miltenyi Biotec). mRNA was enriched using Oligo(dT) beads.
Poly-dT-enrichment, DNAse treatment, chemical fragmentation, ss-Synthesis, strand specific library prep according to: Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Jul 20. doi:10.1093/nar/gkp596
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
S1888_mp_doppel-Kos_4
Strand specific RNA-Seq
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| Data processing |
Read Alignment: pBWA version 0.5.9-r32-MPI-patch2 against mm9 (UCSC)
Counts per feature: Reads per exon were computed using bedtools version 2.11, summarized per gene based on Ensembl Gene 61 annotation.
Normalization of reads per gene: The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.8.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited 'counts' file with sample size normalized counts per gene (rows) and sample (columns)
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| Submission date |
Mar 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Tina Schumann |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of Immunology
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| Department |
Medical Faculty "Carl Gustav Carus"
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| Street address |
Fetscherstraße 74
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| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE45358 |
Gene expression analysis of murine peritoneal macrophages deficient for SAMHD1 and IFNAR |
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| Relations |
| SRA |
SRX253168 |
| BioSample |
SAMN01985463 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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